Red - Game breaking / run ending bugs. Need immediate attention. (FIX TI FIX IT FIX IT)
Yellow - Not game breaking, but are still important and should be addressed.
Green - Do not affect gameplay, or only affect it in a very minor way, but are bugs nonetheless.

(Not complete) List of bugs:

Ending 12 and Challenge 10 still do not unlock after defeating the boss of the Cathedral.
Note: Many players who had previously unlocked these two things had them re-locked after the 1.1(?) patch, and defeating the Cathedral does not unlock them again.

Various unlocks continue to stay locked after completing their requirements.
Note: They possibly unlock(?), but no message appears.
In the ending credits, enemies with alternate versions introduced in Wrath of the Lamb will quickly switch between their different forms, giving them the appearance of spazzing out (i.e. F. hopper and spider hopper, Scolex and Pin).

Upon killing an enemy that drops a pickup (heart, coin, etc), the drop occasionally appears in the top left corner of the room, instead of where the enemy died. Also applies to poop and fire. Other items have also been seen appearing in the top-left corner, such as explosive barrels.
On the Womb / Utero XL, no item is won for beating the boss that comes directly before Mom's Heart.

Challenges 1, 2, and 3 do not unlock the correct achievements on Steam.

Having multiple familiars may cause conflicts with one another, and may not do what they're supposed to do.

Graphical abnormalities occur with certain items when used together, such as flying + SMB Super Fan. Also, Sampson's hair has a tendency to disappear with most items.

Alternate versions of the Cathedral boss don't unlock, despite bringing the polaroid to it.
Using the book of Revelations on XL floors can cause the wrong splash image and item reward in boss fights (e.g. Splash screen shows Pestilence, yet you fight Peep, and after fighting Peep, you get the Cube of Meat.)

Using the Blood Bank or the Devil Beggar while at one red heart will kill the player even if they have soul hearts left to spend. Only occurs on the Womb / Utero / Sheol / Cathedral.

Using the D6 on the first boss of an XL floor will cause the second boss to drop the Cube of Meat.

The music for Fistula and Teratoma doesn't stop after the boss has been defeated.

Technology 2 does not do damage while used in conjunction with Mom's Knife.

There exists a rare bug that deletes a user's save file after a game crash.
The aiming reticule for Epic Fetus may be affected by items such as Mom's Bra or the Hourglass. It also collides with fire.

Secret rooms on XL maps don't always contain the expected "secret room reward." Sometimes they just contain monsters, or are functionally equivalent to a normal room.

One of the alternate final bosses of the Cathedral has a graphical glitch where his head appears to look like his previous form's head.

Under certain circumstances, Pin can regain all of his health during a fight.

Conquest or the Headless Horseman may appear in place of a regular horsemen. The wrong splash screen is sometimes displayed before the fight, and instead of dropping a Pony, a Cube of Meat is dropped instead.

I'm playing right now. Just found brimstone and is sadly not firing with the items I have on in this screenshot I see the animation of Maggie ready to attack but the Brimstone can't be seen nor monsters are affected when targeted.

I'm playing right now. Just found brimstone and is sadly not firing with the items I have on in this screenshot I see the animation of Maggie ready to attack but the Brimstone can't be seen nor monsters are affected when targeted.

Samson isn't spawning with a soul heart for me. That's noteworthy. Also the Book of Sin won't unlock no matter what I do. I don't know if that's a rare bug or what, but I've seen others with the same issue.